Prior to SHU, Skelly was an assistant coach at Binghamton for three seasons. He worked with the defensemen and goalies and helped develop the defensive game plan. As an assistant the Bearcats reached the 2014 America East Tournament and had their highest conference finish since 2004, going 4-1 to finish second. In three seasons, Skelly coached 12 America East All-Conference honorees, six America East All-Rookie Team selections, six America East All-Academic honorees, and two USILA North-South Game participants.

He started his coaching career at his alma mater, The College at Brockport. After graduating in 2010, Skelly served as an assistant coach for the 2012 and 2013 seasons. As Defensive Coordinator, Brockports defense improved both seasons and led the State University of New York Athletic Conference at nine goals per game allowed in 2013. He also coached the programs first All-American, defenseman Collin King. As a player at Brockport, Skelly led the team in ground balls twice and caused turnovers once in 2010. He was a three-time selection to both the SUNYAC Commissioners Academic List and the SUNYAC All-Academic Team.